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Article|19 Jan 2023|OPEN
Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa
Fangping Li1,2 ,† , Shiqiang Xu1 ,† , Zitong Xiao1,2 ,† , Jingming Wang1,2 , Yu Mei1 , Haifei Hu3 , Jingyu Li1 , Jieying Liu2 and Zhuangwei Hou2 , Junliang Zhao3 , Shaohai Yang1 , Jihua Wang,1 ,
1Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crop Research Institute, Guangdong Academy of Agriculture Sciences, Guangzhou 510640, China
2Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
3Rice Research Institute & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
*Corresponding author. E-mail: wangjihua@gdaas.cn
Fangping Li and Shiqiang Xu,Zitong Xiao contributed equally to the study.

Horticulture Research 10,
Article number: uhad005 (2023)
doi: https://doi.org/10.1093/hr/uhad005
Views: 291

Received: 31 Aug 2022
Accepted: 08 Jan 2021
Published online: 19 Jan 2023

Abstract

Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomic breeding of R. tomentosa were hindered by the lack of a reference genome. Here, we presented a chromosome-level gap-free T2T genome assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the genome with size of 470.35 Mb and contig N50 of ~43.80 Mb with 11 pseudochromosomes. A total of 33 382 genes and 239.31 Mb of repetitive sequences were annotated in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process. The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R. tomentosa.